RFdiffusion3 Documentation

RFdiffusion3 is a powerful protein design tool that operates on the atomic level to study ligand-protein interactions, create nucleic acid-protein interfaces, and design de novo enzymes. It is designed to be highly flexible and user-friendly, making it suitable for a wide range of applications in computational biology and biochemistry.

General

• Installation of RFdiffusion3 on Unix Systems
• Inference Calculation Basics
• RFdiffusion3 — Input Specification & Command-line arguments
• Designability vs. Diversity

Introductory Tutorials

These introductory tutorials are designed to help users get familiar with the capabilities of RFD3 for specific design tasks.

• Protein-Protein Interface Design in RFdiffusion3
• Enzyme Design in RFdiffusion3
• Nuclei Acid Binder Design in RFdiffusion3

Intermediate Tutorials

These intermediate tutorials cover more complex topics related to specific design tasks in RFD3. If this is your first time using RFD3, we recommend starting with the introductory tutorials before moving on to these.

• Intermediate Enzyme Design Tutorial

Examples

The following examples demonstrate how to use RFD3 for various design tasks. However, they do not go into detail about how to set up RFD3 or how the different constraints work. If you are new to RFD3, we recommend starting with the introductory tutorials before moving on to these examples.

• RFdiffusion3 — Nucleic acid binder design examples
• RFdiffusion3 — Small molecule binder design examples
• RFdiffusion3 — Protein binder design examples
• Overview of Symmetry in RFD3
• RFdiffusion3 — Enzyme design examples